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Yorodumi- PDB-5eib: Crystal structure of CPAP PN2-3 C-terminal loop-helix in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eib | ||||||
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Title | Crystal structure of CPAP PN2-3 C-terminal loop-helix in complex with DARPin-tubulin | ||||||
Components |
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Keywords | CELL CYCLE / PN2-3 / Tubulin complex | ||||||
Function / homology | Function and homology information astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / motile cilium assembly ...astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / motile cilium assembly / positive regulation of spindle assembly / microtubule nucleation / non-motile cilium assembly / gamma-tubulin binding / positive regulation of axon guidance / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / smoothened signaling pathway / microtubule polymerization / microtubule-based process / centriole replication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / nervous system development / mitotic cell cycle / microtubule / transcription coactivator activity / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / centrosome / GTP binding / protein kinase binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others) Bos taurus (cattle) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, H. / Zheng, X. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Molecular basis for CPAP-tubulin interaction in controlling centriolar and ciliary length Authors: Zheng, X. / Ramani, A. / Soni, K. / Gottardo, M. / Zheng, S. / Ming Gooi, L. / Li, W. / Feng, S. / Mariappan, A. / Wason, A. / Widlund, P. / Pozniakovsky, A. / Poser, I. / Deng, H. / Ou, G. ...Authors: Zheng, X. / Ramani, A. / Soni, K. / Gottardo, M. / Zheng, S. / Ming Gooi, L. / Li, W. / Feng, S. / Mariappan, A. / Wason, A. / Widlund, P. / Pozniakovsky, A. / Poser, I. / Deng, H. / Ou, G. / Riparbelli, M. / Giuliano, C. / Hyman, A.A. / Sattler, M. / Gopalakrishnan, J. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eib.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eib.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eib_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5eib_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5eib_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 5eib_validation.cif.gz | 64.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5eib ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eib | HTTPS FTP |
-Related structure data
Related structure data | 4drxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules CDE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
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#2: Protein | Mass: 49983.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 |
#3: Protein | Mass: 17998.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Protein/peptide , 1 types, 1 molecules F
#4: Protein/peptide | Mass: 2687.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HC77 |
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-Non-polymers , 3 types, 601 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE C201S IS BASED ON REFERENCE 1 OF DATABASE Q6B856 (TBB2B_BOVIN). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: potassium sodium tartrate, PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015 / Details: ADSC Quantum 315r | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 63572 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.653 / Net I/av σ(I): 16.8 / Net I/σ(I): 8.1 / Num. measured all: 291375 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DRX Resolution: 2.1→41.347 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.347 Å
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Refine LS restraints |
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LS refinement shell |
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